domains, baseline
fticr domains
We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)
how many FTICR reps per treatment type?
so we select formulae seen in at least 2 reps per treatment type
unique to each amendment, in each incubation type
overall
#>
#> Call:
#> adonis(formula = relabund_wide %>% select(aliphatic:other) ~ (Amendments + Moisture + Wetting + Suction + Homogenization)^3, data = relabund_wide)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.14469 0.07235 7.749 0.04743 0.001 ***
#> Moisture 1 0.21659 0.21659 23.197 0.07100 0.001 ***
#> Wetting 1 0.00949 0.00949 1.017 0.00311 0.359
#> Suction 1 0.38693 0.38693 41.442 0.12683 0.001 ***
#> Homogenization 1 0.17509 0.17509 18.753 0.05739 0.001 ***
#> Amendments:Moisture 2 0.04272 0.02136 2.288 0.01400 0.053 .
#> Amendments:Wetting 2 0.05755 0.02878 3.082 0.01887 0.017 *
#> Amendments:Suction 2 0.02770 0.01385 1.483 0.00908 0.186
#> Amendments:Homogenization 2 0.13843 0.06921 7.413 0.04538 0.001 ***
#> Moisture:Wetting 1 0.01834 0.01834 1.964 0.00601 0.163
#> Moisture:Suction 1 0.05744 0.05744 6.152 0.01883 0.004 **
#> Moisture:Homogenization 1 0.00569 0.00569 0.610 0.00187 0.586
#> Wetting:Suction 1 0.04324 0.04324 4.631 0.01417 0.015 *
#> Wetting:Homogenization 1 0.05857 0.05857 6.273 0.01920 0.005 **
#> Suction:Homogenization 1 0.02398 0.02398 2.568 0.00786 0.073 .
#> Amendments:Moisture:Wetting 2 0.08924 0.04462 4.779 0.02925 0.002 **
#> Amendments:Moisture:Suction 2 0.03256 0.01628 1.744 0.01067 0.140
#> Amendments:Moisture:Homogenization 2 0.04431 0.02216 2.373 0.01452 0.061 .
#> Amendments:Wetting:Suction 2 0.03546 0.01773 1.899 0.01162 0.097 .
#> Amendments:Wetting:Homogenization 2 0.02015 0.01007 1.079 0.00660 0.370
#> Amendments:Suction:Homogenization 2 0.08434 0.04217 4.517 0.02765 0.004 **
#> Moisture:Wetting:Suction 1 0.02053 0.02053 2.199 0.00673 0.123
#> Moisture:Wetting:Homogenization 1 0.01006 0.01006 1.078 0.00330 0.329
#> Moisture:Suction:Homogenization 1 0.02606 0.02606 2.791 0.00854 0.080 .
#> Wetting:Suction:Homogenization 1 0.01174 0.01174 1.257 0.00385 0.284
#> Residuals 136 1.26979 0.00934 0.41623
#> Total 172 3.05069 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
PERMANOVA for treatments
1.5 kPa intact cores
#>
#> Call:
#> adonis(formula = intact_1_5 %>% select(aliphatic:other) ~ Amendments * Moisture * Wetting, data = intact_1_5)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.00598 0.002992 0.4876 0.01265 0.761
#> Moisture 1 0.07655 0.076546 12.4747 0.16179 0.001 ***
#> Wetting 1 0.05513 0.055131 8.9847 0.11653 0.001 ***
#> Amendments:Moisture 2 0.02610 0.013050 2.1268 0.05517 0.077 .
#> Amendments:Wetting 2 0.04201 0.021005 3.4232 0.08880 0.018 *
#> Moisture:Wetting 1 0.01159 0.011590 1.8888 0.02450 0.136
#> Amendments:Moisture:Wetting 2 0.05326 0.026629 4.3398 0.11257 0.006 **
#> Residuals 33 0.20249 0.006136 0.42800
#> Total 44 0.47311 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
50 kPa intact cores
#>
#> Call:
#> adonis(formula = intact_50 %>% select(aliphatic:other) ~ Amendments * Moisture * Wetting, data = intact_50)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.08911 0.044557 5.8120 0.19613 0.001 ***
#> Moisture 1 0.01105 0.011052 1.4416 0.02432 0.253
#> Wetting 1 0.01364 0.013645 1.7798 0.03003 0.175
#> Amendments:Moisture 2 0.03580 0.017902 2.3352 0.07880 0.064 .
#> Amendments:Wetting 2 0.02310 0.011549 1.5064 0.05084 0.225
#> Moisture:Wetting 1 0.02864 0.028638 3.7355 0.06303 0.029 *
#> Amendments:Moisture:Wetting 2 0.02301 0.011506 1.5008 0.05065 0.231
#> Residuals 30 0.22999 0.007666 0.50620
#> Total 41 0.45436 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1.5 kPa homogenized cores
#>
#> Call:
#> adonis(formula = homo_1_5 %>% select(aliphatic:other) ~ Amendments * Moisture * Wetting, data = homo_1_5)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.11836 0.059179 7.8805 0.16732 0.001 ***
#> Moisture 1 0.20554 0.205538 27.3701 0.29057 0.001 ***
#> Wetting 1 0.01826 0.018258 2.4313 0.02581 0.077 .
#> Amendments:Moisture 2 0.02901 0.014506 1.9317 0.04102 0.106
#> Amendments:Wetting 2 0.04013 0.020065 2.6719 0.05673 0.046 *
#> Moisture:Wetting 1 0.01276 0.012762 1.6995 0.01804 0.167
#> Amendments:Moisture:Wetting 2 0.05051 0.025255 3.3630 0.07140 0.021 *
#> Residuals 31 0.23280 0.007510 0.32910
#> Total 42 0.70737 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
50 kPa homogenized cores
#>
#> Call:
#> adonis(formula = homo_50 %>% select(aliphatic:other) ~ Amendments * Moisture * Wetting, data = homo_50)
#>
#> Permutation: free
#> Number of permutations: 999
#>
#> Terms added sequentially (first to last)
#>
#> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
#> Amendments 2 0.19043 0.095213 6.6889 0.22699 0.001 ***
#> Moisture 1 0.00609 0.006088 0.4277 0.00726 0.668
#> Wetting 1 0.03251 0.032511 2.2839 0.03875 0.128
#> Amendments:Moisture 2 0.07283 0.036415 2.5582 0.08681 0.046 *
#> Amendments:Wetting 2 0.03047 0.015235 1.0703 0.03632 0.407
#> Moisture:Wetting 1 0.00969 0.009687 0.6805 0.01155 0.524
#> Amendments:Moisture:Wetting 2 0.05565 0.027826 1.9548 0.06634 0.101
#> Residuals 31 0.44127 0.014235 0.52599
#> Total 42 0.83893 1.00000
#> ---
#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
individual cores
Date run: 2020-08-10
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#>
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] patchwork_1.0.1 visNetwork_2.0.9 vegan_2.5-6 lattice_0.20-41 permute_0.9-5 rmarkdown_2.3
#> [7] drake_7.12.4 ggbiplot_0.55 PNWColors_0.1.0 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.1
#> [13] purrr_0.3.4 readr_1.3.1 tidyr_1.1.1 tibble_3.0.3 ggplot2_3.3.2 tidyverse_1.3.0
#> [19] here_0.1
#>
#> loaded via a namespace (and not attached):
#> [1] httr_1.4.2 jsonlite_1.7.0 splines_4.0.2 modelr_0.1.8 assertthat_0.2.1 base64url_1.4
#> [7] blob_1.2.1 cellranger_1.1.0 yaml_2.2.1 progress_1.2.2 pillar_1.4.6 backports_1.1.8
#> [13] glue_1.4.1 digest_0.6.25 rvest_0.3.6 colorspace_1.4-1 htmltools_0.5.0 Matrix_1.2-18
#> [19] plyr_1.8.6 pkgconfig_2.0.3 broom_0.7.0 haven_2.3.1 scales_1.1.1 mgcv_1.8-31
#> [25] txtq_0.2.3 generics_0.0.2 farver_2.0.3 ellipsis_0.3.1 withr_2.2.0 cli_2.0.2
#> [31] magrittr_1.5 crayon_1.3.4 readxl_1.3.1 evaluate_0.14 storr_1.2.1 fs_1.5.0
#> [37] fansi_0.4.1 nlme_3.1-148 MASS_7.3-51.6 xml2_1.3.2 tools_4.0.2 prettyunits_1.1.1
#> [43] hms_0.5.3 lifecycle_0.2.0 munsell_0.5.0 reprex_0.3.0 cluster_2.1.0 compiler_4.0.2
#> [49] rlang_0.4.7 grid_4.0.2 rstudioapi_0.11 htmlwidgets_1.5.1 igraph_1.2.5 labeling_0.3
#> [55] gtable_0.3.0 DBI_1.1.0 R6_2.4.1 lubridate_1.7.9 knitr_1.29 utf8_1.1.4
#> [61] filelock_1.0.2 rprojroot_1.3-2 stringi_1.4.6 parallel_4.0.2 Rcpp_1.0.5 vctrs_0.3.2
#> [67] dbplyr_1.4.4 tidyselect_1.1.0 xfun_0.16